Genome wide analysis reveals single nucleotide polymorphisms associated with fatness and putative novel copy number variants in three pig breeds

BMC Genomics

Research Article

Emily J Clemente¹  Nabeel A Affara¹  Christopher P Reitter¹  Julien Bauer¹  Grant A Walling²  Stephen Waite²  Ricardo Pong-Wong³  Darren K Griffin⁴  Katie E Fowler⁴ 

[1] Department of Pathology, University of Cambridge, Tennis Court Road, CB2 1QP, Cambridge, UK;JSR Genetics, Southburn, YO25 9ED, Driffield, East Yorkshirea, UK;Roslin Institute, The University of Edinburgh, Roslin Biocentre, EH25 9PS, Midlothian, Scotland, UK;School of Biosciences, University of Kent, CT2 7NH, Canterbury, Kent, UK;

关键词: SNP;    CNV;    Pig;    QuantiSNP;    cnvPartition;    Fatness;    Obesity;    Genotyping;    GWAS;   

DOI  :  10.1186/1471-2164-14-784

 received in 2013-03-27, accepted in 2013-10-29,  发布年份 2013

来源: Springer

【 摘 要 】

BackgroundObesity, excess fat tissue in the body, can underlie a variety of medical complaints including heart disease, stroke and cancer. The pig is an excellent model organism for the study of various human disorders, including obesity, as well as being the foremost agricultural species. In order to identify genetic variants associated with fatness, we used a selective genomic approach sampling DNA from animals at the extreme ends of the fat and lean spectrum using estimated breeding values derived from a total population size of over 70,000 animals. DNA from 3 breeds (Sire Line Large White, Duroc and a white Pietrain composite line (Titan)) was used to interrogate the Illumina Porcine SNP60 Genotyping Beadchip in order to identify significant associations in terms of single nucleotide polymorphisms (SNPs) and copy number variants (CNVs).ResultsBy sampling animals at each end of the fat/lean EBV (estimate breeding value) spectrum the whole population could be assessed using less than 300 animals, without losing statistical power. Indeed, several significant SNPs (at the 5% genome wide significance level) were discovered, 4 of these linked to genes with ontologies that had previously been correlated with fatness (NTS, FABP6, SST and NR3C2). Quantitative analysis of the data identified putative CNV regions containing genes whose ontology suggested fatness related functions (MCHR1, PPARα, SLC5A1 and SLC5A4).ConclusionsSelective genotyping of EBVs at either end of the phenotypic spectrum proved to be a cost effective means of identifying SNPs and CNVs associated with fatness and with estimated major effects in a large population of animals.

【 授权许可】

Unknown   
© Fowler et al.; licensee BioMed Central Ltd. 2013. This article is published under license to BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.